Isolation of a 167 basepair chromatosome containing a partially digested histone H5

Puigdomènech, Pere; Jose, Matilde; Ruiz-Carrillo, Adolfo; Crane‐Robinson, Colyn

doi:10.1016/0014-5793(83)80893-x

Cited by 19 publications

(9 citation statements)

References 27 publications

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“…Since MNase digestion experiments show that the tails of H5 do not affect the interactions between the globular domain and the nucleosome (Allan et al, 1980; Puigdomenech et al, 1983) and the globular domain in complex with the nucleosome has been used as a model for the chromatosome in earlier studies (Allan et al, 1980; Zhou et al, 1998), we reconstituted the globular domain of H5 (H5 22-98 ) in complex with the nucleosome for structural determination. The nucleosome contains 167 bp DNA centered with the 147 bp ‘601’ positioning sequence (Dorigo et al, 2004; Thastrom et al, 2004).…”

Section: Resultsmentioning

confidence: 99%

“…Either the full-length linker histone H5 or the globular domain (H5 24-98 ) alone can protect the same linker DNA in the native chromatin against micrococcal nuclease (MNase) digestion (Allan et al, 1980; Puigdomenech et al, 1983). Earlier studies of nucleosome recognition by linker histones have focused mainly on how the globular domain of H5 binds to the nucleosome (Allan et al, 1980; Cui and Zhurkin, 2009; Fan and Roberts, 2006; Zhou et al, 1998).…”

Section: Introductionmentioning

confidence: 99%

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Structural Mechanisms of Nucleosome Recognition by Linker Histones

et al. 2015

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Summary Linker histones bind to the nucleosome and regulate the structure of chromatin and gene expression. Despite more than three decades of effort, structural basis of nucleosome recognition by linker histones remains elusive. Here, we report the crystal structure of the globular domain of chicken linker histone H5 in complex with the nucleosome at 3.5 Å resolution, which is validated using nuclear magnetic resonance spectroscopy. The globular domain sits on the dyad of the nucleosome and interacts with both DNA linkers. Our structure integrates results from mutation analyses, previous cross-linking and fluorescence recovery after photobleach experiments, and helps resolve the long debate on structural mechanisms of nucleosome recognition by linker histones. The on-dyad binding mode of the H5 globular domain is different from the recently reported off-dyad binding mode of Drosophila linker histone H1. We demonstrate that linker histones with different binding modes could fold chromatin to form distinct higher-order structures.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Structural Mechanisms of Nucleosome Recognition by Linker Histones

et al. 2015

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“…Either the full-length linker histone H5 or GH5 alone can protect the same native chromatin linker DNA from micrococcal nuclease digestion [23,39]. Recently, we combined X-ray crystallography and NMR to investigate the structural mechanism of nucleosome recognition by GH5 and found that it binds to the nucleosome on the dyad [40].…”

Section: Introductionmentioning

confidence: 99%

A Small Number of Residues Can Determine if Linker Histones Are Bound On or Off Dyad in the Chromatosome

Zhou

Feng

Ghirlando

et al. 2016

Journal of Molecular Biology

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Linker histones bind to the nucleosome and regulate the structure and function of chromatin. We have previously shown that the globular domains of chicken H5 and Drosophila H1 linker histones bind to the nucleosome with on- or off-dyad modes, respectively. To explore the determinant for the distinct binding modes, we investigated the binding of a mutant globular domain of H5 to the nucleosome. This mutant, termed GH5_pMut, includes substitutions of five globular domain residues of H5 with the corresponding residues in the globular domain of Drosophila H1. The residues at these five positions play important roles in nucleosome binding by either H5 or Drosophila H1. NMR and spin-labeling experiments showed that GH5_pMut bound to the nucleosome off the dyad. We further found that the nucleosome array condensed by either the GH5_pMut or the globular domain of Drosophila H1 displayed a similar sedimentation coefficient, whereas the same nucleosome array condensed by the wild-type globular domain of H5 showed a much larger sedimentation coefficient. Moreover, NMR and spin-labeling results from the study of the nucleosome in complex with the full-length human linker histone H1.0, whose globular domain shares high sequence conservation with the corresponding globular domain of H5, are consistent with an on-dyad binding mode. Taken together, our results suggest that a small number of residues in the globular domain of a linker histone can control its binding location on the nucleosome and higher-order chromatin structure.

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“…Interestingly, although the C-terminal tail determines the organization of higher-order chromatin structures (17,23) and the binding geometry of the linker DNA (17,18) it does not appear to affect the LH positioning around the dyad (17). Moreover, the full length LH and the isolated globular domain protect the same L-DNA from micrococcal nuclease digestion (24), indicating that the globular domain determines the binding geometry, whereas the C-terminal tail further refines the interaction with the linker DNA. H5 is an avian LH that differs in sequence from mammalian LH isoforms, but shares most similarity with human H1.0, which is mostly found in terminally differentiated cells (see sequence alignment in Supplementary Data).…”

Section: Introductionmentioning

confidence: 99%

Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome

et al. 2016

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Linker histones are essential for DNA compaction in chromatin. They bind to nucleosomes in a 1:1 ratio forming chromatosomes. Alternative configurations have been proposed in which the globular domain of the linker histone H5 (gH5) is positioned either on- or off-dyad between the nucleosomal and linker DNAs. However, the dynamic pathways of chromatosome assembly remain elusive. Here, we studied the conformational plasticity of gH5 in unbound and off-dyad nucleosome-bound forms with classical and accelerated molecular dynamics simulations. We find that the unbound gH5 converts between open and closed conformations, preferring the closed form. However, the open gH5 contributes to a more rigid chromatosome and restricts the motion of the nearby linker DNA through hydrophobic interactions with thymidines. Moreover, the closed gH5 opens and reorients in accelerated simulations of the chromatosome. Brownian dynamics simulations of chromatosome assembly, accounting for a range of amplitudes of nucleosome opening and different nucleosome DNA sequences, support the existence of both on- and off-dyad binding modes of gH5 and reveal alternative, sequence and conformation-dependent chromatosome configurations. Taken together, these findings suggest that the conformational dynamics of linker histones and nucleosomes facilitate alternative chromatosome configurations through an interplay between induced fit and conformational selection.

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Isolation of a 167 basepair chromatosome containing a partially digested histone H5

Cited by 19 publications

References 27 publications

Structural Mechanisms of Nucleosome Recognition by Linker Histones

Structural Mechanisms of Nucleosome Recognition by Linker Histones

A Small Number of Residues Can Determine if Linker Histones Are Bound On or Off Dyad in the Chromatosome

Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome

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